The movies are in tif format but the motion correction was fine. cisTEM works with tif format? since I didn't get any error. When I started CTF estimation I didn't get any error in GUI. When the CTF estimation starts in GUI it is said that all 13 processes are connected. All slaves have reconnected to the master and then after 2-3 min the GUI will be closed and I got this message in terminal: Master socket disconnected. I was using cisTEM before and I didn't have problem. The only difference is that I have the movies in mrc format now I have them in tif. I don't know if this causes a problem.

Yes, I did the motion correction and it worked fine. I also tried CTF estimation with another data set that I had in mrc format and it was ok. I don't know maybe it doesn't work with this tif format. But if doesn't work why I didn't get any error when I was importing the movies or doing motion correction?

I did the 3D classification and at the end I got 6 classes but when I looked at the classes, class 3 and 5 was good and I wanted to do another 3D classification on these two classes but I don't know how can I select particles of these two classes. Could you please tell me how I can do it?